Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019621.1 Corchorus olitorius cultivar O-4 contig19654, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 74504
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:667 original size:13 final size:14
Alignment explanation
Indices: 624--669 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
614 AATGTATCGC
624 AAAACTTCTTTGAA
1 AAAACTTCTTTGAA
**
638 AAAACTTC-TTGTC
1 AAAACTTCTTTGAA
651 AAAACTTCTTTGAA
1 AAAACTTCTTTGAA
665 AAAAC
1 AAAAC
670 AATCATCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACTTCTTTGAA
Found at i:2735 original size:3 final size:3
Alignment explanation
Indices: 2721--2769 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
2711 CATTATTGTG
* * * *
2721 TTA TTG TTA TTA TTA TTA TAA TTA TTG TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2769 T
1 T
2770 AATAATAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2747 original size:21 final size:21
Alignment explanation
Indices: 2721--2760 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2711 CATTATTGTG
2721 TTATTGTTATTATTATTATAA
1 TTATTGTTATTATTATTATAA
2742 TTATTGTTATTATTATTAT
1 TTATTGTTATTATTATTAT
2761 TATAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
TTATTGTTATTATTATTATAA
Found at i:2770 original size:6 final size:6
Alignment explanation
Indices: 2729--2788 Score: 50
Period size: 6 Copynumber: 10.2 Consensus size: 6
2719 TGTTATTGTT
* * * * * *
2729 ATTATT ATTATA ATTATT GTTATT ATTATT ATTATA ATTATA ATAATA
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA
*
2777 ATAATA A-TATA A
1 ATTATA ATTATA A
2789 AATAAGCTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
5 4 0.09
6 43 0.91
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTATA
Found at i:6509 original size:15 final size:15
Alignment explanation
Indices: 6489--6531 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
6479 GGTTTCTTTC
6489 TCTTTTTTTTTCCTT
1 TCTTTTTTTTTCCTT
*
6504 TCTTTTTTGTTCCTT
1 TCTTTTTTTTTCCTT
6519 TCTTTTTCTTTTC
1 TCTTTTT-TTTTC
6532 AATGGCATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (15 bp):
TCTTTTTTTTTCCTT
Found at i:11638 original size:48 final size:47
Alignment explanation
Indices: 11563--11706 Score: 159
Period size: 49 Copynumber: 3.0 Consensus size: 47
11553 GAGCGTGCCA
* * * * *
11563 ATCAATTTTATCCAAAAATTGATAAAAAGTGCGA-TGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG
11610 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG
* * *
11659 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGT-AAAGTAAAAG
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
11705 AT
1 AT
11707 TGCTTGGAGT
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
46 10 0.12
47 14 0.17
48 18 0.21
49 41 0.49
50 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Found at i:26397 original size:76 final size:76
Alignment explanation
Indices: 26247--26390 Score: 177
Period size: 76 Copynumber: 1.9 Consensus size: 76
26237 ACAAGGACCC
* * *
26247 CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
26312 GGGCAGTGTCA
66 GGGCAGTGTCA
* * **
26323 CGACTCCAGCTGGGCGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
26385 GATGGG
63 GATGGG
26391 TTGTGTCTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.07
76 48 0.83
77 6 0.10
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:34182 original size:21 final size:21
Alignment explanation
Indices: 34153--34218 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
34143 GCACACTTTT
*
34153 CAATTGATTGAAATTTCATTA
1 CAATCGATTGAAATTTCATTA
* *
34174 CAATCGATTG-AATCTTCCTTT
1 CAATCGATTGAAAT-TTCATTA
* *
34195 CAATCGATTGAAATTGCTTTA
1 CAATCGATTGAAATTTCATTA
34216 CAA
1 CAA
34219 CTTGCTGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 3 0.08
21 31 0.84
22 3 0.08
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (21 bp):
CAATCGATTGAAATTTCATTA
Found at i:35878 original size:27 final size:27
Alignment explanation
Indices: 35848--35924 Score: 154
Period size: 27 Copynumber: 2.9 Consensus size: 27
35838 CATTGGGGAC
35848 ATCCAGGGGCATTTTGGTCATTTGCAT
1 ATCCAGGGGCATTTTGGTCATTTGCAT
35875 ATCCAGGGGCATTTTGGTCATTTGCAT
1 ATCCAGGGGCATTTTGGTCATTTGCAT
35902 ATCCAGGGGCATTTTGGTCATTT
1 ATCCAGGGGCATTTTGGTCATTT
35925 CAAGTACACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (27 bp):
ATCCAGGGGCATTTTGGTCATTTGCAT
Found at i:38648 original size:41 final size:41
Alignment explanation
Indices: 38590--38687 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
38580 CTTCTTCTTC
*
38590 AATTTAGTCCCTAATTTAGGATTCTATTTACTATTTGATAT
1 AATTTAGTCCCTAATTTAGGATTCTAGTTACTATTTGATAT
* *
38631 AATTTAGTCCCTGATTTAGGATTTTAGTTACTATTTGAT-T
1 AATTTAGTCCCTAATTTAGGATTCTAGTTACTATTTGATAT
*
38671 CAATTTGGT-CCTAATTT
1 -AATTTAGTCCCTAATTT
38688 GTCTTTATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
40 8 0.16
41 43 0.84
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (41 bp):
AATTTAGTCCCTAATTTAGGATTCTAGTTACTATTTGATAT
Found at i:43188 original size:29 final size:29
Alignment explanation
Indices: 43143--43200 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
43133 TCAGGCCGCT
43143 AAGGATTTGAGGCAATTAAAATTTCAGTG
1 AAGGATTTGAGGCAATTAAAATTTCAGTG
* *
43172 AAGGATTTGAGGTAATTAAAATTTTAGTG
1 AAGGATTTGAGGCAATTAAAATTTCAGTG
43201 GGGTCAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
AAGGATTTGAGGCAATTAAAATTTCAGTG
Found at i:45312 original size:19 final size:18
Alignment explanation
Indices: 45269--45303 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
45259 TTTGGATTAT
45269 AATTAAATAATAGTAAATC
1 AATTAAAT-ATAGTAAATC
45288 AATTAAAT-TAGTAAAT
1 AATTAAATATAGTAAAT
45304 TCAAATTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
AATTAAATATAGTAAATC
Found at i:45430 original size:17 final size:19
Alignment explanation
Indices: 45388--45438 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
45378 AATTTTTAAG
45388 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
45407 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
45425 TTAAATAAT-TAATA
1 -TAAA-AATATAATA
45439 GTCGGGTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.14
19 22 0.76
20 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:45791 original size:17 final size:15
Alignment explanation
Indices: 45753--45792 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
45743 AACAATATCT
45753 TATATATAATTTTAA
1 TATATATAATTTTAA
*
45768 TACATATAATTTTAAA
1 TATATATAATTTT-AA
45784 TATTATATA
1 TA-TATATA
45793 TGATTAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 4 0.19
17 5 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATAATTTTAA
Found at i:45843 original size:15 final size:15
Alignment explanation
Indices: 45825--45853 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45815 TATAGTTTAA
45825 TATATTATATATAAC
1 TATATTATATATAAC
45840 TATATTATATATAA
1 TATATTATATATAA
45854 TTTTAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATTATATATAAC
Found at i:45844 original size:17 final size:17
Alignment explanation
Indices: 45803--45877 Score: 60
Period size: 19 Copynumber: 4.0 Consensus size: 17
45793 TGATTAAAAC
*
45803 CTATATATTATATATAGT
1 CTATATATTATATATA-A
*
45821 TTAATATATTATATATAA
1 CT-ATATATTATATATAA
*
45839 CTATATTATATATAATTTTAAA
1 CTATA-TAT-TAT-A-TAT-AA
45861 CTATATATTATATATAA
1 CTATATATTATATATAA
45878 TTTCATAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
17 5 0.11
18 7 0.15
19 18 0.39
20 4 0.09
21 5 0.11
22 7 0.15
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (17 bp):
CTATATATTATATATAA
Found at i:61763 original size:40 final size:41
Alignment explanation
Indices: 61706--61822 Score: 155
Period size: 41 Copynumber: 2.9 Consensus size: 41
61696 ATCAATTTCT
* * *
61706 AAAATCAGGGACTAAATTGCATC-AAGAGTAAATAAAATCC
1 AAAAGCAGGGATTAAATTGCATCAAATAGTAAATAAAATCC
*
61746 TAAAGCAGGGATTAAATTGCATCAAATAGTAAATAAAATCC
1 AAAAGCAGGGATTAAATTGCATCAAATAGTAAATAAAATCC
** * *
61787 AAAATAAGGGATCAAATTGAATCAAATAGTAAATAA
1 AAAAGCAGGGATTAAATTGCATCAAATAGTAAATAA
61823 GATATTAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 20 0.30
41 47 0.70
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAAGCAGGGATTAAATTGCATCAAATAGTAAATAAAATCC
Found at i:64108 original size:15 final size:15
Alignment explanation
Indices: 64088--64119 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
64078 ATTGTTATCC
*
64088 TTTACTGTTTACTCT
1 TTTACTGATTACTCT
64103 TTTACTGATTACTCT
1 TTTACTGATTACTCT
64118 TT
1 TT
64120 ACTCTTTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.59
Consensus pattern (15 bp):
TTTACTGATTACTCT
Found at i:64155 original size:21 final size:22
Alignment explanation
Indices: 64131--64182 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
64121 CTCTTTGTCA
*
64131 TTACCATTTTACTGGTTAC-TG
1 TTACCATTTTACTGATTACTTG
* *
64152 TTACTC-CTTTACTGATTACTTT
1 TTAC-CATTTTACTGATTACTTG
64174 TTACCATTT
1 TTACCATTT
64183 CTTGATTACT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.19, C:0.21, G:0.08, T:0.52
Consensus pattern (22 bp):
TTACCATTTTACTGATTACTTG
Found at i:64176 original size:35 final size:35
Alignment explanation
Indices: 64080--64177 Score: 94
Period size: 35 Copynumber: 2.8 Consensus size: 35
64070 TTTTGCTCAT
*
64080 TGTTA-TCCTTTACTGTTTACTCTTTTACTGATTAC
1 TGTTACTCCTTTACTGATTACT-TTTTACTGATTAC
* * * * *
64115 TCTTTACT-CTTT-GTCATTACCATTTTACTGGTTAC
1 T-GTTACTCCTTTACTGATTA-CTTTTTACTGATTAC
64150 TGTTACTCCTTTACTGATTACTTTTTAC
1 TGTTACTCCTTTACTGATTACTTTTTAC
64178 CATTTCTTGA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
34 5 0.10
35 29 0.60
36 13 0.27
37 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.08, T:0.53
Consensus pattern (35 bp):
TGTTACTCCTTTACTGATTACTTTTTACTGATTAC
Found at i:64436 original size:33 final size:33
Alignment explanation
Indices: 64376--64493 Score: 159
Period size: 32 Copynumber: 3.6 Consensus size: 33
64366 CTCTTTAATT
**
64376 CTAATTACTATTTTA-AGTTTTGAATTTGATTG
1 CTAATTACTATTTTACCCTTTTGAATTTGATTG
*
64408 CTAATTACTATTTTACCCTTTTGGATTTGATTG
1 CTAATTACTATTTTACCCTTTTGAATTTGATTG
* *
64441 CTAATTACTATTTTACCC-TTTGAAATTGATTT
1 CTAATTACTATTTTACCCTTTTGAATTTGATTG
* *
64473 CTAGTTACCATTTTACCCTTT
1 CTAATTACTATTTTACCCTTT
64494 ACTGACTAAC
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
32 42 0.55
33 34 0.45
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.51
Consensus pattern (33 bp):
CTAATTACTATTTTACCCTTTTGAATTTGATTG
Found at i:65073 original size:21 final size:21
Alignment explanation
Indices: 65004--65073 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
64994 AATGTGGAAG
65004 CCCAACAGAATAAAAACAAGA
1 CCCAACAGAATAAAAACAAGA
** * ***
65025 CCCAAACCCATTTAATATGGAAG-
1 CCC-AACAGA-ATAA-AAACAAGA
65048 CCCAACAGAATAAAAACAAGA
1 CCCAACAGAATAAAAACAAGA
65069 CCCAA
1 CCCAA
65074 ACCCATTTGA
Statistics
Matches: 33, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 4 0.12
21 11 0.33
22 8 0.24
23 6 0.18
24 4 0.12
ACGTcount: A:0.53, C:0.27, G:0.10, T:0.10
Consensus pattern (21 bp):
CCCAACAGAATAAAAACAAGA
Found at i:65118 original size:44 final size:44
Alignment explanation
Indices: 64957--65098 Score: 203
Period size: 44 Copynumber: 3.2 Consensus size: 44
64947 ATATTAAGAG
* * * **
64957 GCCCAACAGAAAGTAAAAACAAGACCCAAGCCTATGTAATGTGGAA
1 GCCCAACAG-AA-TAAAAACAAGACCCAAACCCATTTAACATGGAA
*
65003 GCCCAACAGAATAAAAACAAGACCCAAACCCATTTAATATGGAA
1 GCCCAACAGAATAAAAACAAGACCCAAACCCATTTAACATGGAA
*
65047 GCCCAACAGAATAAAAACAAGACCCAAACCCATTTGACATGGAA
1 GCCCAACAGAATAAAAACAAGACCCAAACCCATTTAACATGGAA
65091 GCCCAACA
1 GCCCAACA
65099 AAAAAGATTA
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 79 0.88
45 2 0.02
46 9 0.10
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.12
Consensus pattern (44 bp):
GCCCAACAGAATAAAAACAAGACCCAAACCCATTTAACATGGAA
Found at i:70200 original size:2 final size:2
Alignment explanation
Indices: 70193--70225 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
70183 ACATGTAAAG
70193 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
70226 TGAAGTGCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73783 original size:27 final size:27
Alignment explanation
Indices: 73717--73818 Score: 125
Period size: 27 Copynumber: 3.7 Consensus size: 27
73707 TAAGGTCATT
* * *
73717 CAGGGGCATTTTGGTCATTTTTCA-ATTA
1 CAGGGGCATTTTAGTCA-TTTGCACA-TC
*
73745 CAGGGGCATTTTGGTCATTTGCACATC
1 CAGGGGCATTTTAGTCATTTGCACATC
*
73772 CAGGGGCATTTTAGTCATTTGCACGTC
1 CAGGGGCATTTTAGTCATTTGCACATC
*
73799 CAGGGGCATTCTAGTCATTT
1 CAGGGGCATTTTAGTCATTT
73819 TAAGTTCACA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
27 50 0.74
28 18 0.26
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (27 bp):
CAGGGGCATTTTAGTCATTTGCACATC
Done.